they are at no disadvantage BECAUSE the league strength is accounted for.
All you have to do is look at the Trinity league. Those non MD/SJB teams would otherwise be really low seeds, or in their system, D2. Orange Lutheran, serra, and santa margarita all 2-3 in league, 6-4 overall, serra is 5-5, and all top 17 in state. All in Southern Section's D1 playoff.
If the league strength in the SFL wasn't accounted for, they'd possibly all be unjustifiably seeded too low, and there'd be uproar about how Jesuit is seeded above Del Oro.
DO and Rocklln got byes because they are in D2... and it's hard to argue they aren't top 4 in D2. In fact, I'd argue Rocklin should've been 3 over Downey... but since they split DO and Rocklin, they bumped Rocklin down to 4. When DO was in D1, they were the 7 and 10 seed. So that is evidence against your argument. You could argue Jesuit should be above Rocklin, and that would bolster your argument. But they both should be above Downey, which would've given Rocklin a bye anyways.
League strength can be accounted for, of course. But you are missing that the creation of the unbalanced leagues is the problem that I am actually complaining about. When a team is placed in a league, they are essentially stuck there, for good or for bad. The benefits of being a bottom feeder in a super-league outweighs the benefits of competing in a weak league. Any of Whitney's losses in league will always be better than Laguna Creek's wins. Whether this is actually true or not doesn't matter. This year it was. Next year, maybe not.
This would all be fine IF there was some type of relegation/promotion system in place. The easy proof of that is exactly what happened with Grant this year. They were over matched in the SFL. They leave for the Metro and their whole mindset changes. Imagine a system that makes this a fundamental part of its structure.
As an example, let's make a 12 team Delta and resurrect the old Delta River (A league) and Delta Valley (B league) within it. You could go even bigger and make it 18 teams with three sub-leagues, but not in this post.
Fill the sub-leagues like this (Davis, River City, or other teams could also be used):
Delta River
Folsom
Oak Ridge
Monterey Trail
Elk Grove
Jesuit
Sheldon
Delta Valley
Laguna Creek
Cosumnes Oaks
Franklin
Pleasant Grove
McClatchy
Kennedy
That's five league games PLUS each team in each sub-league has to play at least one pre-season game against a team in the other. That still leaves four other pre-league games and no in-league byes. Traditional rivalries could be created and maintained that way.
Now, whomever finishes in the bottom one or two spots in the Delta River gets moved down to the Delta Valley and the same number of teams come up. It could be done every year or two, but definitely more often than full re-alignment.
So in this scenario, when a team in the Delta River is given a benefit due to being in a strong league, they EARNED it, at least to some extent. The Delta River could be given more automatic playoff berths or just benefit from overall league strength for at-large bids. The winner of the Delta Valley would get an automatic bid, for sure. Additionally, any team that schedules well and wins a lot would still be eligible for an at-large bid.
12 or 18 team clusters could be created throughout the section combining any manner of divisions within it as makes sense. Imagine a Sierra league that had Sierra Foothill and Sierra View sub-leagues with teams like Granite Bay, Del Oro, Rocklin, Grant. Antelope, Woodcreek, Whitney, Inderkum, Roseville, etc. The "Strong League" advantage would be earned and teams would maintain strength or cycle accordingly.
Placing teams into particular divisions for playoffs is another post. This model does not directly address that. It would be too long to go into here.